T U T O R I A L - Biopathways and Petri Nets
Preliminaries
The following material is provided for the benefit of the participants
of the
tutorial
"Qualitative Modelling and Analysis of Biochemical Pathways
with
Petri Nets",
given at the 5th Int. Conference on Systems Biology, Heidelberg,
on Saturday, October 9, 2004, 10.00 - 13.00.
In case you want to use your own laptop during the tutorial, we
recommend to download in advance the following material. Especially,
the
software tools provided will allow you to immediately experience the
principles and techniques presented. In case you prefer a dry
introduction into the subject, just download and print the slides.
Downloads
(1) tutorial_slides.pdf
Hint: To make the slides self-contained, they contain more
material than it will be discussed in the tutorial.
The following software tools are available free of charge for academic
purposes. In the tutorial, we use the Windows versions, only.
(2) Snoopy - a software tool to design and animate hierarchical Petri
nets. The
tool has been developed, and is still under development, at the
University of Technology in Cottbus, Dep. of Computer Science,
chair "data structures and software dependability".
Follow the given simple installation procedure given
here.
There is no manual available, but you will probably
not miss it.
(3) INA - the Integrated
Net Analyzer - is used to to analyze the Petri nets produced by
Snoopy. The tool has been developed at the Humboldt
University in Berlin, Dep. of Computer Science, chair "automata
theory" over about 20 years. So it shouldn't be a big surprise that it
comes along with a
pure ASCII user interface only.
INA.exe
for Windows (recommended)
INA
manual
(not
necessarily required)
No special installation procedure is required. Just start INA on a
command line of a DOS window by typing its name.
Recommendations - to
make live easy:
- rename INAwin32.exe to ina.exe;
- write the ina.exe in the same folder as snoopy.exe,
or better: add the directory, where ina.exe is located, to the
PATH system variable;
Good luck, and see you soon in Heidelberg.
Ina.Koch(at)tfh-berlin.de
Monika.Heiner(at)informatik.tu-cottbus.de
. . . t h e e n d . . .